TiMet is part of an expanding network of plant systems biology projects around the world. We aim to be a useful contact point for news, knowledge exchange and discussion. Please join the conversation!
TiMet Participant Portal
TiMet Participant Portal
TiMet assembles world leaders in experimental and theoretical plant systems biology to advance understanding of the regulatory interactions between the circadian clock and plant metabolism, and their emergent effects on whole-plant growth and productivity.
TiMet - Linking the Clock to Metabolism is a Collaborative Project (Grant Agreement 245143) funded by the European Commission FP7, in response to call FP7-KBBE-2009-3.
TiMet is part of an expanding network of plant systems biology projects around the world. We aim to be a useful contact point for news, knowledge exchange and discussion. Please join the conversation!
To facilitate the dissemination of our work, we conducted two online tutorials on how to use the Framework Model on the 2nd and 5th of December 2014. These tutorials were intended for plants scientists, systems biologists and modellers, to whom we introduced the FM and our online resources. A total →
Tomasz Zielinski (UEDIN) attended OpenBIS training in Basel, Switzerland. OpenBIS is an open source system for managing biological information that is being used in over 20 institutions. The training was focused on features of OpenBIS from the power-user perspective, like: system configuration, metadata →
Earlier this week (September 23-24) the Lithuanian Presidency of the EU Council held an international conference on the “Horizons for Social Sciences and Humanities“ in Vilnius. Participants discussed the ways to address the most pressing global challenges and to define the roles of social sciences →
As a prelude to our recent Annual Meeting, held this year at The Centre for Research in Agricultural Genomics (CRAG) in Barcelona, TiMet hosted a workshop attended by the leaders of eight other projects and nine industry stakeholders, all involved in EU FP7 projects funded under the KBBE (knowledge →
TiMet is advancing understanding of how plants regulate the use of carbon for growth and productivity. We combine quantitative biology and computational modelling to explore the interaction of the circadian clock and key metabolic pathways that regulate leaf and root growth in the model plant Arabidopsis thaliana. Our work will contribute to the construction of multi-scale models of plant growth that can predict performance in response to environmental cues.
Clock-regulated pathways coordinate the response of many developmental processes to changes in photoperiod →
Plant growth involves the coordinated distribution of carbon resources both towards structural components →
Understanding how dynamic molecular networks affect whole-organism physiology, analogous to mapping →
Trehalose 6-phosphate (Tre6P), the intermediate of trehalose biosynthesis, has a profound influence →
The maximum yield of crop plants depends on the efficiency of conversion of sunlight into biomass. This →
Growth is driven by newly fixed carbon in the light, but depends at night on reserves, like starch, →
Natural genetic diversity provides a powerful tool to study the complex interrelationship between metabolism →
The timing of the induction of flowering determines to a large extent the reproductive success of plants →
The maximum yield of crop plants depends on the efficiency of conversion of sunlight into biomass. This →
Abstract: Plants grow in a light/dark cycle. We have investigated how growth is buffered against the →
TiMet experiments on temperature compensation of starch breakdown have provided important insights into →
This review provides an update on the pathways of starch synthesis and degradation, presents emerging →
Plants capture energy and assimilate carbon – via photosynthesis – in the light, but cannot do so in the dark. They buffer these daily fluctuations in their carbon budget by storing some of the assimilated carbon as starch in their leaves and by utilising it as a carbon supply during the night.
Proteaceae species in south-western Australia occur on phosphorus- (P) impoverished soils. Their leaves →
Plant growth involves the coordinated distribution of carbon resources both towards structural components →
Arabidopsis (Arabidopsis thaliana) leaves synthesize starch faster in short days than in long days, →
Experiments were designed to compare the relationship between starch degradation and the use of carbon →
The first step on the pathway of starch degradation in Arabidopsis (Arabidopsis thaliana) leaves at →
Trehalose 6-phosphate (Tre6P), the intermediate of trehalose biosynthesis, has a profound influence →
In many plants, starch is synthesized during the day and degraded during the night to avoid carbohydrate →
Trehalose is a quantitatively important compatible solute and stress protectant in many organisms, including →
Background: Plant biomass consists primarily of carbohydrates derived from photosynthesis. Monitoring →
In short photoperiods plants accumulate starch more rapidly in the light and degrade it more slowly →
Many plants accumulate substantial starch reserves in their leaves during the day, and remobilise them →
Photosynthetic starch reserves that accumulate in Arabidopsis leaves during the day decrease approximately →
Growth is driven by newly fixed carbon in the light, but depends at night on reserves, like starch, →
Glycans comprise ubiquitous and essential biopolymers, which usually occur as highly diverse mixtures →
Abstract: Plants grow in a light/dark cycle. We have investigated how growth is buffered against the →
TiMet experiments on temperature compensation of starch breakdown have provided important insights into →
ADP-glucose pyrophosphorylase (AGPase) catalyses the first committed step in the pathway of starch synthesis →
This review provides an update on the pathways of starch synthesis and degradation, presents emerging →
Isoprenoids represent a diverse group of plant metabolites, with a host of structural and functional roles that are critical to plant growth, development and survival.
Isoprenoid molecules are essential elements of plant metabolism. Many important plant isoprenoids, such →
Carotenoids are plastidial isoprenoids essential for the protection of photosynthetic tissues against →
Plants use two pathways for the production of the same universal isoprenoid precursors: the mevalonic →
Multiple geranylgeranyl diphosphate synthases (GGPPS) for biosynthesis of geranylgeranyl diphosphate →
The ability to interpret daily and seasonal alterations in light and temperature signals is essential →
Borderline personality disorder (BPD) was first described 75 years ago (Stern, 1938), but only became →
Plastids provide plants with metabolic pathways that are unique among eukaryotes, including the methylerythritol →
Isoprenoid biosynthesis is essential for all living organisms, and isoprenoids are also of industrial →
Geranylgeranyl diphosphate (GGPP) is a key precursor of various isoprenoids that have diverse functions →
Isoprenoids are a large family of compounds synthesized by all free-living organisms. In most bacteria →
Isoprenoids are functionally and structurally the most diverse group of plant metabolites reported to →
Abstract: Plant carotenoids are a family of pigments that participate in light harvesting and are essential →
This update article discusses some of the most recent advances in the plant isoprenoid field, focusing →
Plants must orchestrate the accumulation and utilisation of photosynthetic products over the daily cycle to avoid periods of starvation, and thus optimise growth rates. Discovering the mechanism by which the circadian clock exercises control over metabolism is essential if we are to find new ways to enhance plant productivity. TiMet scientists are developing new computational models of the gene regulatory networks that operate in the Arabidopsis thaliana circadian clock.
The circadian clock is an important molecular mechanism that enables many organisms to anticipate and →
Clock-regulated pathways coordinate the response of many developmental processes to changes in photoperiod →
The circadian clock measures time across a 24 h period, increasing fitness by phasing biological processes →
We assess the accuracy of three established regression methods for reconstructing gene and protein →
Abstract We assess the accuracy of various state-of-the-art statistics and machine learning methods →
In many plants, starch is synthesized during the day and degraded during the night to avoid carbohydrate →
The ability to interpret daily and seasonal alterations in light and temperature signals is essential →
24-hour biological clocks are intimately connected to the cellular signalling network, which complicates →
This paper reports the use of luciferase reporter gene imaging to monitor circadian rhythms in leaves →
In many organisms, the circadian clock is composed of functionally coupled morning and evening oscillators →
Abstract: Plants grow in a light/dark cycle. We have investigated how growth is buffered against the →
The P2011 clock model fundamentally revises the clock gene circuit, notably due to the inclusion of →
The stochastic model of Guerriero et al. addresses single-cell behaviour, for the first time in a plant →
Rapid progress in the field of theoretical systems biology underpins Timet’s efforts to model pathways and networks. Integrating different approaches is important to develop consistent theoretical descriptions encompassing various scales of biological information.
The circadian clock is an important molecular mechanism that enables many organisms to anticipate and →
Isoprenoid molecules are essential elements of plant metabolism. Many important plant isoprenoids, such →
Parameter inference in mechanistic models based on systems of coupled differential equations is a topical →
We assess the accuracy of three established regression methods for reconstructing gene and protein →
Abstract We assess the accuracy of various state-of-the-art statistics and machine learning methods →
In many plants, starch is synthesized during the day and degraded during the night to avoid carbohydrate →
The circadian clock is an important molecular mechanism that enables many organisms to anticipate →
In the light, photosynthesis provides carbon for metabolism and growth. In the dark, plant growth depends →
An important and challenging problem in systems biology is the inference of gene regulatory networks →
Many biochemical reactions are confined to interfaces, such as membranes or cell walls. Despite their →
System integration of metabolism is considered in analogy to the investigation of corporate misdemeanour →
To relax the homogeneity assumption of classical dynamic Bayesian networks (DBNs), various recent studies →
24-hour biological clocks are intimately connected to the cellular signalling network, which complicates →
Researchers affiliated to TiMet have been tracking the metabolic fate of carbon in plant leaves, and →
Glycans comprise ubiquitous and essential biopolymers, which usually occur as highly diverse mixtures →
Here the authors describe a semi-flexible model based on a piecewise homogeneous dynamic Bayesian network →
In this paper, the authors introduce a Bayesian regularization scheme that addresses the problem of →
The P2011 clock model fundamentally revises the clock gene circuit, notably due to the inclusion of →
The stochastic model of Guerriero et al. addresses single-cell behaviour, for the first time in a plant →
Dynamic Bayesian networks (DBNs) have been applied widely to reconstruct the structure of regulatory →
TiMet’s data infrastructure supports the biological research data workflow by facilitating cross-domain queries for all data, metadata, and associated models. The TiMetDB data warehouse architecture builds on a design implemented for the EU Framework 6 AGRON-OMICS project.
We have made publicly available the new version of our service for circadian research: BioDare2. It →
Tomasz Zielinski (UEDIN) attended OpenBIS training in Basel, Switzerland. OpenBIS is an open source →
BioDare was developed by the BBSRC/EPSRC‐funded ROBuST SABR project and it functionality further improved →
A key step in the analysis of circadian data is to make an accurate estimate of the underlying period →
Circadian biology is a major area of research in many species. One of the key objectives of data analysis →
Abstract: A substantial part of the AGRON-OMICS consortium is devoted to profiling the growing Arabidopsis →
TiMet users have access to the Agron-omics Leaf Database, the data integration and data sharing portal →
The Arabidopsis thaliana Isoprenoid Pathway Database (AtIPD; http://www.atipd.ethz.ch) can be searched →
Many datasets of importance to TiMet are deposited in the BioDare Biological Data Repository, which →
PlaSMo (Plant System Biology Modelling) provides TiMet with a central resource of current plant based →
TiMetDB (login required) is the central database, analysis and modelling platform of the consortium. →
Integrating mathematical models of biochemical and gene networks can link cell-level regulation to an emergent property (plant growth) at whole organism level. Such multi-scale modelling is a major goal for plant systems biology.
This model is termed P2012 and derives from the article: Modelling the widespread effects of TOC1 signalling →
The model is publicly available from the Biomodels database and from the PlaSMo model repository: →
The model is publicly available from the PlaSMo model repository, with multiple versions, as PLM_47 →
New knowledge inspires collaboration, prioritises experimental effort, provides new hypotheses, and informs experimental designs.
Proteaceae species in south-western Australia occur on phosphorus- (P) impoverished soils. Their leaves →
The circadian clock is an important molecular mechanism that enables many organisms to anticipate and →
Isoprenoid molecules are essential elements of plant metabolism. Many important plant isoprenoids, such →
Carotenoids are plastidial isoprenoids essential for the protection of photosynthetic tissues against →
Clock-regulated pathways coordinate the response of many developmental processes to changes in photoperiod →
Plant growth involves the coordinated distribution of carbon resources both towards structural components →
The circadian clock measures time across a 24 h period, increasing fitness by phasing biological processes →
Plants use two pathways for the production of the same universal isoprenoid precursors: the mevalonic →
Multiple geranylgeranyl diphosphate synthases (GGPPS) for biosynthesis of geranylgeranyl diphosphate →
Arabidopsis (Arabidopsis thaliana) leaves synthesize starch faster in short days than in long days, →
Experiments were designed to compare the relationship between starch degradation and the use of carbon →
Understanding how dynamic molecular networks affect whole-organism physiology, analogous to mapping →
Parameter inference in mechanistic models based on systems of coupled differential equations is a topical →
We assess the accuracy of three established regression methods for reconstructing gene and protein →
The first step on the pathway of starch degradation in Arabidopsis (Arabidopsis thaliana) leaves at →
Trehalose 6-phosphate (Tre6P), the intermediate of trehalose biosynthesis, has a profound influence →
A key step in the analysis of circadian data is to make an accurate estimate of the underlying period →
Circadian biology is a major area of research in many species. One of the key objectives of data analysis →
Abstract We assess the accuracy of various state-of-the-art statistics and machine learning methods →
The inference of gene co-expression networks is a valuable resource for novel hypotheses in experimental →
In many plants, starch is synthesized during the day and degraded during the night to avoid carbohydrate →
The ability to interpret daily and seasonal alterations in light and temperature signals is essential →
Borderline personality disorder (BPD) was first described 75 years ago (Stern, 1938), but only became →
Trehalose is a quantitatively important compatible solute and stress protectant in many organisms, including →
The circadian clock is an important molecular mechanism that enables many organisms to anticipate →
Information about the abundance and biological activities of proteins is essential to reveal how genes →
The maximum yield of crop plants depends on the efficiency of conversion of sunlight into biomass. This →
Proteaceae species in south-western Australia occur on phosphorus- (P) impoverished soils. Their leaves →
Background: Plant biomass consists primarily of carbohydrates derived from photosynthesis. Monitoring →
In the light, photosynthesis provides carbon for metabolism and growth. In the dark, plant growth depends →
An important and challenging problem in systems biology is the inference of gene regulatory networks →
Plastids provide plants with metabolic pathways that are unique among eukaryotes, including the methylerythritol →
In short photoperiods plants accumulate starch more rapidly in the light and degrade it more slowly →
Many plants accumulate substantial starch reserves in their leaves during the day, and remobilise them →
Many biochemical reactions are confined to interfaces, such as membranes or cell walls. Despite their →
Photosynthetic starch reserves that accumulate in Arabidopsis leaves during the day decrease approximately →
Isoprenoid biosynthesis is essential for all living organisms, and isoprenoids are also of industrial →
Geranylgeranyl diphosphate (GGPP) is a key precursor of various isoprenoids that have diverse functions →
Growth is driven by newly fixed carbon in the light, but depends at night on reserves, like starch, →
System integration of metabolism is considered in analogy to the investigation of corporate misdemeanour →
Isoprenoids are a large family of compounds synthesized by all free-living organisms. In most bacteria →
To relax the homogeneity assumption of classical dynamic Bayesian networks (DBNs), various recent studies →
Natural genetic diversity provides a powerful tool to study the complex interrelationship between metabolism →
24-hour biological clocks are intimately connected to the cellular signalling network, which complicates →
Researchers affiliated to TiMet have been tracking the metabolic fate of carbon in plant leaves, and →
The timing of the induction of flowering determines to a large extent the reproductive success of plants →
The maximum yield of crop plants depends on the efficiency of conversion of sunlight into biomass. This →
Isoprenoids are functionally and structurally the most diverse group of plant metabolites reported to →
This paper reports the use of luciferase reporter gene imaging to monitor circadian rhythms in leaves →
Glycans comprise ubiquitous and essential biopolymers, which usually occur as highly diverse mixtures →
In many organisms, the circadian clock is composed of functionally coupled morning and evening oscillators →
Abstract: Plants grow in a light/dark cycle. We have investigated how growth is buffered against the →
Abstract: Plant carotenoids are a family of pigments that participate in light harvesting and are essential →
Abstract: A substantial part of the AGRON-OMICS consortium is devoted to profiling the growing Arabidopsis →
Here the authors describe a semi-flexible model based on a piecewise homogeneous dynamic Bayesian network →
In this paper, the authors introduce a Bayesian regularization scheme that addresses the problem of →
The P2011 clock model fundamentally revises the clock gene circuit, notably due to the inclusion of →
The stochastic model of Guerriero et al. addresses single-cell behaviour, for the first time in a plant →
Dynamic Bayesian networks (DBNs) have been applied widely to reconstruct the structure of regulatory →
The Arabidopsis thaliana Isoprenoid Pathway Database (AtIPD; http://www.atipd.ethz.ch) can be searched →
TiMet experiments on temperature compensation of starch breakdown have provided important insights into →
ADP-glucose pyrophosphorylase (AGPase) catalyses the first committed step in the pathway of starch synthesis →
This review provides an update on the pathways of starch synthesis and degradation, presents emerging →
This update article discusses some of the most recent advances in the plant isoprenoid field, focusing →
TiMet assembles world leaders in experimental and theoretical plant systems biology to advance understanding of the regulatory interactions between the circadian clock and plant metabolism, and their emergent effects on whole-plant growth and productivity.
Samuel C Zeeman is Professor of Plant Biochemistry at ETH Zurich, Switzerland. He is an expert in →
Dirk Husmeier holds a Chair in Statistics in the School of Mathematics and Statistics at the University →
Oliver Ebenhoeh is Reader in Systems Biology, a joint position of the Institute for Complex Systems →
Manuel Rodríguez-Concepcion is an expert in isoprenoid metabolism. He and his group at the Center →
Prof. Mark Stitt and his group at the Max Planck Institute of Molecular Plant Physiology (MPIMP) →
Wilhelm Gruissem, Professor of Plant Biotechnology at ETH Zurich, Switzerland, is a world expert in →
Alison Smith is Head of the Department of Metabolic Biology at the John Innes Centre in Norwich, →
Andrew Millar holds a Chair of Systems Biology in SynthSys at the University of Edinburgh, UK. He →
The TiMet consortium brings together leading centres for the emerging discipline of Systems Biology, at a European and world scale.
TiMet is one of several EU-funded projects that collectively contribute to Europe’s knowledge-based bio-economy (KBBE) by bringing together science, industry and other stakeholders to generate and exploit new knowledge related to plant and crop growth and productivity.
To facilitate the dissemination of our work, we conducted two online tutorials on how to use the Framework →
Symposium and Workshop on Modelling Wheat Under Changing Environment: Model Intercomparison and Improvement →
CropM International Symposium and Workshop: Modelling climate change impacts on crop production for →
If photorespiration could be reduced in current C3 crops, or if they could be converted to use C4 photosynthesis →
Understanding of root-to-shoot signalling and source-sink relationships; Exploitation of natural genetic →
Making use of joint phenotyping and modelling platforms, EURoot's objective is to enhance the cereal →
Resistance of crops to combined abiotic and biotic stress (legumes).
Developing novel methods and strategies for genetic yield improvement under dry environments and →
Impact of environmental conditions on epigenetic states (maize).
Genetic and molecular tools for plant breeding (tomato and maize).
Genes underlying important plant traits (Solanaceae).
Secondary metabolites / isoprenoids (Solanaceae).
Molecular components driving growth.
TiMet is part of an expanding network of plant systems biology projects around the world. We aim to be a useful contact point for knowledge exchange and discussion